This is a good link to learn about using PowerShell Mangement (SharePoint Designer) with BDC in SharePoint 2010.
http://blogs.msdn.com/b/bcs/archive/2010/02/16/bcs-powershell-introduction-and-throttle-management.aspx
In Lionelro's topic, he explained and show you what about limitation of number items in BDC when you are using SharePoint Designer and PowerShell. However, I want to show you a short term to change the default limitation using PowerShell.
Start PowerShell Management
Run these scripts:
$dbRule = Get-SPBusinessDataCatalogThrottleConfig -ScopeDatabase -ThrottleType Items -ServiceApplicationProxy$bdcProxy
#Default and Maximum must be provided together. This increases the limit for external lists to 3000.
Set-SPBusinessDataCatalogThrottleConfig -Identity $dbRule -Maximum 1000000 -Default 3000
Just execute above commands it will change the default limitation of number items when you get the data from BDC.
Good luck.
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